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Suffolk County judges have freed at least 11 defendants facing drug charges, almost all with lengthy criminal ­records, since early September, in the first wave of potentially thousands of cases that have been gravely compromised by the burgeoning scandal at the state drug lab.

All the defendants were in jail awaiting trial on charges related to selling cocaine, heroin, or other drugs, but judges agreed to release them or drastically reduce their bail because evidence in their ­cases was analyzed by Annie Dookhan, the state chemist accused of altering test results and mishandling evidence. Charges against the defendants were not dropped, but defense attorneys say it is unlikely their clients can ever be convicted, based on evidence that could be tainted.

“We have an obligation to protect every defendant’s constitutional rights, and we embrace it,” Suffolk District Attorney Daniel F. Conley said. “But we can’t lose sight of the massive public safety implications here. A large number of dangerous individuals could be released right back to our streets and neighborhoods.”

Some of the prisoners who could soon be released include “high-level dealers, violent felons, and armed gunmen,” Conley said.

A Suffolk County drug defendant who had already pleaded guilty, David Huffman, will ask a judge Monday to set him free because of Dookhan’s involve­ment. In Norfolk Superior Court in ­Dedham, judges have already agreed to similar requests by two men serving time on drug charges, including David Danielli, who went free this week, 2½ years early, on charges related to selling oxycodone pills.

The releases begin as Attorney General Martha Coakley launches an inves­tigation into whether the problems with the now-closed state lab, which was run by the Department of Public Health in Jamaica Plain, go beyond the alleged mishandling of up to 60,000 drug samples by Dookhan. Standard practice required that two chemists sign off on each analysis, raising questions about whether any of her co-workers failed to catch the errors or botched their own testing, said a source with direct knowledge of the lab’s operation.

“This is one of the largest criminal [problems] in the history of the Commonwealth,” said Norfolk District Attorney Michael W. Morrissey. “It will shake the entire foundation of the system. We’re faced with very difficult and complex decisions on thousands of cases. Our focus is on people who are wrongfully incarcerated, though I’m not suggesting they are not guilty. If you can’t use the evidence, a lot of the cases are going to be toast.”

Prosecutors and defense attor­neys alike say that it is not yet clear how many cases may have been compromised and whether Dookhan’s mere signature on lab results will require the analysis to be thrown out. But sorting the issues out on a case-by-case basis, they say, will be time-consuming and potentially expensive.

“We’re giving each case and each defendant the attention they deserve, but with tens of thousands of samples potentially compromised, that ­approach won’t be sustainable for long,” Conley said. “That’s half our annual caseload.”

Dookhan resigned in March as state officials moved to fire her amid allegations that she had ­improperly removed drug evidence from the storage area. But in July, State Police investigators discovered that Dookhan’s potential misconduct was far greater than previously believed and that she may have deliberately altered the weight of drug samples and purposely mishandled samples for reasons that are still unclear.

The state lab has been closed since August, and a lab supervisor has been fired while Public Health Commissioner John Auerbach and a second lab supervisor have resigned over the failure of supervision. A third lab official, Dookhan’s direct supervisor, is facing civil service disciplinary proceedings. Dookhan, who has not been charged with anything yet, has not responded to ­repeated requests for comment.

But Dookhan’s alleged misconduct has cast a pall over thousands of drug convictions and pending drug trials across Eastern Massachusetts, especially in Boston. Nearly 23,000 of the 60,000 drug samples that Dookhan helped analyze were in Suffolk County.

In addition, a spokeswoman for US Attorney Carmen M. ­Ortiz said her office also sent samples to the Boston lab for testing and has begun a case-by-case review to determine whether Dookhan undermined those cases.

On Friday, Governor Deval Patrick named a former Suffolk County prosecutor, David Meier, to lead a team of law enforce­ment officials and ­defense lawyers scouring cases to determine which must be ­reopened.

Meanwhile, state prosecutors are looking into what role, if any, other chemists in the DPH lab may have had in mishandling evidence. Previously, public health officials had branded Dookhan as a “rogue” chemist acting alone.

“The question is whether the problem is not Annie Dookhan, but a lab problem,” said Bernard Grossberg, who represents Huffman, a convicted drug dealer now in prison.

Huffman, 55, who has a 19-page record dating to 1975, pleaded guilty to trafficking in cocaine and heroin, unlawful possession of a firearm, and other charges and was sentenced to seven to 10 years, ­until the Dookhan allegations surfaced later in August. On Monday, Grossberg will ask a judge to release Huffman and put off sentencing while the drug lab investigation continues. It is unlikely that the convictions will survive, Grossberg said.

“He was elated,” Grossberg said. “He doesn't want to get his hopes up until he gets to court. But she contaminated the drugs. It’s not a situation where the drugs can be retested.”

Grossberg said whether Huffman or any of his other clients are guilty of the crime is not the point. “We’re not talking about guilty,” he said. “It’s whether or not the Commonwealth can prove its allegations. I’m getting calls from ­clients I haven’t spoken to in years. It’s a mess.”

Attorney Susan Rayburn said that her client, Juan Irene, 51, should have been released months ago when prosecutors first realized that Dookhan had potentially mishandled evidence in a large number of drug cases. Irene, who has been in jail for months awaiting trial on charges of selling heroin to an undercover officer, was not released until Sept. 6, when an assistant district attorney made the request in light of Dookhan’s role in analyzing the drug evidence against Irene.

“I don’t think it’s right to wait until the media got a hold of the issue in August and then act like you’re so concerned” about defendants’ rights, said Rayburn, who added that she was referring to ­senior prosecutors. “For months, we were fed little bits of information, ­always with an eye to minimizing” the misconduct by Dookhan, Rayburn said.

Although her client still technically faces drug charges, Rayburn doubts the case can come to trial.

“We can’t put evidence before the jury that we are unsure of,” she explained. “We cannot put evidence before the court that has her name on it.”

Marcus Pixley was freed, over the objection of the Suffolk district attorney, after his $5,000 bail was reduced to $1,000 on Sept. 12. Pixley, 51, was arrested on charges of selling crack to an undercover officer and resisting arrest on Feb. 27, 2011. He has a long criminal record that includes convictions for selling cocaine, rape, and other charges and was deemed a habitual offender.

Pixley’s lawyer, Veronica White, said Pixley had been held for 13 months with severe medical problems on a case built on tainted evidence.

“When the government puts someone in an 8-by-7-foot cell and tells them when they will sleep and eat and wake up, it’s the most intrusive thing you can do to somebody,” said White, adding that she will also fight to clear other clients whose cases also hinged on drugs tested by Dookhan.

“All of these cases that come out of that lab are presumptively tainted,” she said. “You can’t limit every­thing to Annie Dookhan. There are other people who should be held account­able.”

With many more defendants expected to ask to be set free, Conley said the court system has to come up with a comprehensive approach. Otherwise, the disputed caseload could become overwhelming.

“We’re going to need the ­resources to assign full-time personnel to assess each defendant’s conviction or bail status and make a fully informed decision on how to proceed,” Conley said.

Kay Lazar of the Globe staff contributed to this report. ­Andrea Estes can be reached at ­estes@globe.com. ScottAllen can be reached at allen@globe.com.

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